1 2 /* 3 Defines projective product routines where A is a MPIAIJ matrix 4 C = P^T * A * P 5 */ 6 7 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 8 #include <../src/mat/utils/freespace.h> 9 #include <../src/mat/impls/aij/mpi/mpiaij.h> 10 #include <petscbt.h> 11 #include <petsctime.h> 12 13 /* #define PTAP_PROFILE */ 14 15 PetscErrorCode MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer) 16 { 17 PetscErrorCode ierr; 18 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 19 Mat_PtAPMPI *ptap=a->ptap; 20 PetscBool iascii; 21 PetscViewerFormat format; 22 23 PetscFunctionBegin; 24 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 25 if (iascii) { 26 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 27 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 28 if (ptap->algType == 0) { 29 ierr = PetscViewerASCIIPrintf(viewer,"using scalable MatPtAP() implementation\n");CHKERRQ(ierr); 30 } else if (ptap->algType == 1) { 31 ierr = PetscViewerASCIIPrintf(viewer,"using nonscalable MatPtAP() implementation\n");CHKERRQ(ierr); 32 } 33 } 34 } 35 ierr = (ptap->view)(A,viewer);CHKERRQ(ierr); 36 PetscFunctionReturn(0); 37 } 38 39 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 40 { 41 PetscErrorCode ierr; 42 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 43 Mat_PtAPMPI *ptap=a->ptap; 44 45 PetscFunctionBegin; 46 if (ptap) { 47 Mat_Merge_SeqsToMPI *merge=ptap->merge; 48 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 49 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 50 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 51 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 52 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 53 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 54 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 55 if (ptap->AP_loc) { /* used by alg_rap */ 56 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 57 ierr = PetscFree(ap->i);CHKERRQ(ierr); 58 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 59 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 60 } else { /* used by alg_ptap */ 61 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 62 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 63 } 64 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 65 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 66 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 67 68 if (merge) { /* used by alg_ptap */ 69 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 70 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 71 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 72 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 73 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 74 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 75 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 76 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 77 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 78 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 79 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 80 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 81 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 82 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 83 } 84 85 ierr = ptap->destroy(A);CHKERRQ(ierr); 86 ierr = PetscFree(ptap);CHKERRQ(ierr); 87 } 88 PetscFunctionReturn(0); 89 } 90 91 PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 92 { 93 PetscErrorCode ierr; 94 PetscBool flg; 95 MPI_Comm comm; 96 #if !defined(PETSC_HAVE_HYPRE) 97 const char *algTypes[2] = {"scalable","nonscalable"}; 98 PetscInt nalg=2; 99 #else 100 const char *algTypes[3] = {"scalable","nonscalable","hypre"}; 101 PetscInt nalg=3; 102 #endif 103 PetscInt pN=P->cmap->N,alg=1; /* set default algorithm */ 104 105 PetscFunctionBegin; 106 /* check if matrix local sizes are compatible */ 107 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 108 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Arow (%D, %D) != Prow (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); 109 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Acol (%D, %D) != Prow (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); 110 111 if (scall == MAT_INITIAL_MATRIX) { 112 /* pick an algorithm */ 113 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 114 PetscOptionsObject->alreadyprinted = PETSC_FALSE; /* a hack to ensure the option shows in '-help' */ 115 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 116 ierr = PetscOptionsEnd();CHKERRQ(ierr); 117 118 if (!flg && pN > 100000) { /* may switch to scalable algorithm as default */ 119 MatInfo Ainfo,Pinfo; 120 PetscInt nz_local; 121 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 122 123 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 124 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 125 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 126 127 if (pN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 128 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 129 130 if (alg_scalable) { 131 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 132 } 133 } 134 135 switch (alg) { 136 case 1: 137 /* do R=P^T locally, then C=R*A*P */ 138 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 139 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 140 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 141 break; 142 #if defined(PETSC_HAVE_HYPRE) 143 case 2: 144 /* Use boomerAMGBuildCoarseOperator */ 145 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 146 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr); 147 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 148 break; 149 #endif 150 default: 151 /* do R=P^T locally, then C=R*A*P */ 152 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 153 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(A,P,fill,C);CHKERRQ(ierr); 154 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 155 break; 156 } 157 } 158 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 159 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 160 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 161 PetscFunctionReturn(0); 162 } 163 164 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C) 165 { 166 PetscErrorCode ierr; 167 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 168 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 169 Mat_SeqAIJ *ap,*p_loc,*p_oth,*c_seq; 170 Mat_PtAPMPI *ptap = c->ptap; 171 Mat AP_loc,C_loc,C_oth; 172 PetscInt i,rstart,rend,cm,ncols,row,*api,*apj,am = A->rmap->n,apnz; 173 PetscScalar *apa; 174 const PetscInt *cols; 175 const PetscScalar *vals; 176 177 PetscFunctionBegin; 178 ierr = MatZeroEntries(C);CHKERRQ(ierr); 179 180 /* 1) get R = Pd^T,Ro = Po^T */ 181 if (ptap->reuse == MAT_REUSE_MATRIX) { 182 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 183 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 184 } 185 186 /* 2) get AP_loc */ 187 AP_loc = ptap->AP_loc; 188 ap = (Mat_SeqAIJ*)AP_loc->data; 189 190 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 191 /*-----------------------------------------------------*/ 192 if (ptap->reuse == MAT_REUSE_MATRIX) { 193 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 194 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 195 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 196 } 197 198 /* 2-2) compute numeric A_loc*P - dominating part */ 199 /* ---------------------------------------------- */ 200 /* get data from symbolic products */ 201 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 202 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 203 else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ptap->P_oth is NULL. Cannot proceed!"); 204 205 api = ap->i; 206 apj = ap->j; 207 for (i=0; i<am; i++) { 208 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 209 apnz = api[i+1] - api[i]; 210 apa = ap->a + api[i]; 211 ierr = PetscMemzero(apa,sizeof(PetscScalar)*apnz);CHKERRQ(ierr); 212 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa); 213 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 214 } 215 216 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 217 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 218 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 219 220 C_loc = ptap->C_loc; 221 C_oth = ptap->C_oth; 222 223 /* add C_loc and Co to to C */ 224 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 225 226 /* C_loc -> C */ 227 cm = C_loc->rmap->N; 228 c_seq = (Mat_SeqAIJ*)C_loc->data; 229 cols = c_seq->j; 230 vals = c_seq->a; 231 232 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 233 /* when there are no off-processor parts. */ 234 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 235 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 236 /* a table, and other, more complex stuff has to be done. */ 237 if (C->assembled) { 238 C->was_assembled = PETSC_TRUE; 239 C->assembled = PETSC_FALSE; 240 } 241 if (C->was_assembled) { 242 for (i=0; i<cm; i++) { 243 ncols = c_seq->i[i+1] - c_seq->i[i]; 244 row = rstart + i; 245 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 246 cols += ncols; vals += ncols; 247 } 248 } else { 249 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 250 } 251 252 /* Co -> C, off-processor part */ 253 cm = C_oth->rmap->N; 254 c_seq = (Mat_SeqAIJ*)C_oth->data; 255 cols = c_seq->j; 256 vals = c_seq->a; 257 for (i=0; i<cm; i++) { 258 ncols = c_seq->i[i+1] - c_seq->i[i]; 259 row = p->garray[i]; 260 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 261 cols += ncols; vals += ncols; 262 } 263 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 264 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 265 266 ptap->reuse = MAT_REUSE_MATRIX; 267 PetscFunctionReturn(0); 268 } 269 270 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 271 { 272 PetscErrorCode ierr; 273 Mat_PtAPMPI *ptap; 274 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 275 MPI_Comm comm; 276 PetscMPIInt size,rank; 277 Mat Cmpi,P_loc,P_oth; 278 PetscFreeSpaceList free_space=NULL,current_space=NULL; 279 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 280 PetscInt *lnk,i,k,pnz,row,nsend; 281 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 282 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 283 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 284 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 285 MPI_Request *swaits,*rwaits; 286 MPI_Status *sstatus,rstatus; 287 PetscLayout rowmap; 288 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 289 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 290 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi; 291 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 292 PetscScalar *apv; 293 PetscTable ta; 294 MatType mtype; 295 #if defined(PETSC_USE_INFO) 296 PetscReal apfill; 297 #endif 298 299 PetscFunctionBegin; 300 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 301 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 302 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 303 304 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 305 306 /* create symbolic parallel matrix Cmpi */ 307 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 308 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 309 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 310 311 /* create struct Mat_PtAPMPI and attached it to C later */ 312 ierr = PetscNew(&ptap);CHKERRQ(ierr); 313 ptap->reuse = MAT_INITIAL_MATRIX; 314 ptap->algType = 0; 315 316 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 317 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 318 /* get P_loc by taking all local rows of P */ 319 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 320 321 ptap->P_loc = P_loc; 322 ptap->P_oth = P_oth; 323 324 /* (0) compute Rd = Pd^T, Ro = Po^T */ 325 /* --------------------------------- */ 326 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 327 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 328 329 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 330 /* ----------------------------------------------------------------- */ 331 p_loc = (Mat_SeqAIJ*)P_loc->data; 332 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 333 334 /* create and initialize a linked list */ 335 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 336 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 337 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 338 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 339 340 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 341 342 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 343 if (ao) { 344 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 345 } else { 346 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 347 } 348 current_space = free_space; 349 nspacedouble = 0; 350 351 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 352 api[0] = 0; 353 for (i=0; i<am; i++) { 354 /* diagonal portion: Ad[i,:]*P */ 355 ai = ad->i; pi = p_loc->i; 356 nzi = ai[i+1] - ai[i]; 357 aj = ad->j + ai[i]; 358 for (j=0; j<nzi; j++) { 359 row = aj[j]; 360 pnz = pi[row+1] - pi[row]; 361 Jptr = p_loc->j + pi[row]; 362 /* add non-zero cols of P into the sorted linked list lnk */ 363 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 364 } 365 /* off-diagonal portion: Ao[i,:]*P */ 366 if (ao) { 367 ai = ao->i; pi = p_oth->i; 368 nzi = ai[i+1] - ai[i]; 369 aj = ao->j + ai[i]; 370 for (j=0; j<nzi; j++) { 371 row = aj[j]; 372 pnz = pi[row+1] - pi[row]; 373 Jptr = p_oth->j + pi[row]; 374 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 375 } 376 } 377 apnz = lnk[0]; 378 api[i+1] = api[i] + apnz; 379 380 /* if free space is not available, double the total space in the list */ 381 if (current_space->local_remaining<apnz) { 382 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 383 nspacedouble++; 384 } 385 386 /* Copy data into free space, then initialize lnk */ 387 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 388 389 current_space->array += apnz; 390 current_space->local_used += apnz; 391 current_space->local_remaining -= apnz; 392 } 393 /* Allocate space for apj and apv, initialize apj, and */ 394 /* destroy list of free space and other temporary array(s) */ 395 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 396 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 397 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 398 399 /* Create AP_loc for reuse */ 400 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 401 402 #if defined(PETSC_USE_INFO) 403 if (ao) { 404 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 405 } else { 406 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 407 } 408 ptap->AP_loc->info.mallocs = nspacedouble; 409 ptap->AP_loc->info.fill_ratio_given = fill; 410 ptap->AP_loc->info.fill_ratio_needed = apfill; 411 412 if (api[am]) { 413 ierr = PetscInfo3(ptap->AP_loc,"Scalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 414 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 415 } else { 416 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 417 } 418 #endif 419 420 /* (2-1) compute symbolic Co = Ro*AP_loc */ 421 /* ------------------------------------ */ 422 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 423 424 /* (3) send coj of C_oth to other processors */ 425 /* ------------------------------------------ */ 426 /* determine row ownership */ 427 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 428 rowmap->n = pn; 429 rowmap->bs = 1; 430 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 431 owners = rowmap->range; 432 433 /* determine the number of messages to send, their lengths */ 434 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 435 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 436 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 437 438 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 439 coi = c_oth->i; coj = c_oth->j; 440 con = ptap->C_oth->rmap->n; 441 proc = 0; 442 for (i=0; i<con; i++) { 443 while (prmap[i] >= owners[proc+1]) proc++; 444 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 445 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 446 } 447 448 len = 0; /* max length of buf_si[], see (4) */ 449 owners_co[0] = 0; 450 nsend = 0; 451 for (proc=0; proc<size; proc++) { 452 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 453 if (len_s[proc]) { 454 nsend++; 455 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 456 len += len_si[proc]; 457 } 458 } 459 460 /* determine the number and length of messages to receive for coi and coj */ 461 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 462 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 463 464 /* post the Irecv and Isend of coj */ 465 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 466 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 467 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 468 for (proc=0, k=0; proc<size; proc++) { 469 if (!len_s[proc]) continue; 470 i = owners_co[proc]; 471 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 472 k++; 473 } 474 475 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 476 /* ---------------------------------------- */ 477 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 478 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 479 480 /* receives coj are complete */ 481 for (i=0; i<nrecv; i++) { 482 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 483 } 484 ierr = PetscFree(rwaits);CHKERRQ(ierr); 485 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 486 487 /* add received column indices into ta to update Crmax */ 488 for (k=0; k<nrecv; k++) {/* k-th received message */ 489 Jptr = buf_rj[k]; 490 for (j=0; j<len_r[k]; j++) { 491 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 492 } 493 } 494 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 495 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 496 497 /* (4) send and recv coi */ 498 /*-----------------------*/ 499 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 500 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 501 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 502 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 503 for (proc=0,k=0; proc<size; proc++) { 504 if (!len_s[proc]) continue; 505 /* form outgoing message for i-structure: 506 buf_si[0]: nrows to be sent 507 [1:nrows]: row index (global) 508 [nrows+1:2*nrows+1]: i-structure index 509 */ 510 /*-------------------------------------------*/ 511 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 512 buf_si_i = buf_si + nrows+1; 513 buf_si[0] = nrows; 514 buf_si_i[0] = 0; 515 nrows = 0; 516 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 517 nzi = coi[i+1] - coi[i]; 518 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 519 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 520 nrows++; 521 } 522 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 523 k++; 524 buf_si += len_si[proc]; 525 } 526 for (i=0; i<nrecv; i++) { 527 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 528 } 529 ierr = PetscFree(rwaits);CHKERRQ(ierr); 530 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 531 532 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 533 ierr = PetscFree(len_ri);CHKERRQ(ierr); 534 ierr = PetscFree(swaits);CHKERRQ(ierr); 535 ierr = PetscFree(buf_s);CHKERRQ(ierr); 536 537 /* (5) compute the local portion of Cmpi */ 538 /* ------------------------------------------ */ 539 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 540 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 541 current_space = free_space; 542 543 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 544 for (k=0; k<nrecv; k++) { 545 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 546 nrows = *buf_ri_k[k]; 547 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 548 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 549 } 550 551 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 552 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 553 for (i=0; i<pn; i++) { 554 /* add C_loc into Cmpi */ 555 nzi = c_loc->i[i+1] - c_loc->i[i]; 556 Jptr = c_loc->j + c_loc->i[i]; 557 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 558 559 /* add received col data into lnk */ 560 for (k=0; k<nrecv; k++) { /* k-th received message */ 561 if (i == *nextrow[k]) { /* i-th row */ 562 nzi = *(nextci[k]+1) - *nextci[k]; 563 Jptr = buf_rj[k] + *nextci[k]; 564 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 565 nextrow[k]++; nextci[k]++; 566 } 567 } 568 nzi = lnk[0]; 569 570 /* copy data into free space, then initialize lnk */ 571 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 572 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 573 } 574 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 575 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 576 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 577 578 /* local sizes and preallocation */ 579 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 580 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 581 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 582 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 583 584 /* members in merge */ 585 ierr = PetscFree(id_r);CHKERRQ(ierr); 586 ierr = PetscFree(len_r);CHKERRQ(ierr); 587 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 588 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 589 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 590 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 591 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 592 593 /* attach the supporting struct to Cmpi for reuse */ 594 c = (Mat_MPIAIJ*)Cmpi->data; 595 c->ptap = ptap; 596 ptap->duplicate = Cmpi->ops->duplicate; 597 ptap->destroy = Cmpi->ops->destroy; 598 ptap->view = Cmpi->ops->view; 599 600 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 601 Cmpi->assembled = PETSC_FALSE; 602 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 603 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 604 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 605 *C = Cmpi; 606 PetscFunctionReturn(0); 607 } 608 609 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 610 { 611 PetscErrorCode ierr; 612 Mat_PtAPMPI *ptap; 613 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 614 MPI_Comm comm; 615 PetscMPIInt size,rank; 616 Mat Cmpi; 617 PetscFreeSpaceList free_space=NULL,current_space=NULL; 618 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 619 PetscInt *lnk,i,k,pnz,row,nsend; 620 PetscBT lnkbt; 621 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 622 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 623 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 624 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 625 MPI_Request *swaits,*rwaits; 626 MPI_Status *sstatus,rstatus; 627 PetscLayout rowmap; 628 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 629 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 630 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 631 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 632 PetscScalar *apv; 633 PetscTable ta; 634 MatType mtype; 635 #if defined(PETSC_USE_INFO) 636 PetscReal apfill; 637 #endif 638 639 PetscFunctionBegin; 640 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 641 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 642 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 643 644 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 645 646 /* create symbolic parallel matrix Cmpi */ 647 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 648 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 649 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 650 651 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 652 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 653 654 /* create struct Mat_PtAPMPI and attached it to C later */ 655 ierr = PetscNew(&ptap);CHKERRQ(ierr); 656 ptap->reuse = MAT_INITIAL_MATRIX; 657 ptap->algType = 1; 658 659 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 660 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 661 /* get P_loc by taking all local rows of P */ 662 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 663 664 /* (0) compute Rd = Pd^T, Ro = Po^T */ 665 /* --------------------------------- */ 666 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 667 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 668 669 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 670 /* ----------------------------------------------------------------- */ 671 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 672 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 673 674 /* create and initialize a linked list */ 675 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 676 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 677 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 678 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 679 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 680 681 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 682 683 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 684 if (ao) { 685 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 686 } else { 687 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 688 } 689 current_space = free_space; 690 nspacedouble = 0; 691 692 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 693 api[0] = 0; 694 for (i=0; i<am; i++) { 695 /* diagonal portion: Ad[i,:]*P */ 696 ai = ad->i; pi = p_loc->i; 697 nzi = ai[i+1] - ai[i]; 698 aj = ad->j + ai[i]; 699 for (j=0; j<nzi; j++) { 700 row = aj[j]; 701 pnz = pi[row+1] - pi[row]; 702 Jptr = p_loc->j + pi[row]; 703 /* add non-zero cols of P into the sorted linked list lnk */ 704 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 705 } 706 /* off-diagonal portion: Ao[i,:]*P */ 707 if (ao) { 708 ai = ao->i; pi = p_oth->i; 709 nzi = ai[i+1] - ai[i]; 710 aj = ao->j + ai[i]; 711 for (j=0; j<nzi; j++) { 712 row = aj[j]; 713 pnz = pi[row+1] - pi[row]; 714 Jptr = p_oth->j + pi[row]; 715 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 716 } 717 } 718 apnz = lnk[0]; 719 api[i+1] = api[i] + apnz; 720 if (ap_rmax < apnz) ap_rmax = apnz; 721 722 /* if free space is not available, double the total space in the list */ 723 if (current_space->local_remaining<apnz) { 724 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 725 nspacedouble++; 726 } 727 728 /* Copy data into free space, then initialize lnk */ 729 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 730 731 current_space->array += apnz; 732 current_space->local_used += apnz; 733 current_space->local_remaining -= apnz; 734 } 735 /* Allocate space for apj and apv, initialize apj, and */ 736 /* destroy list of free space and other temporary array(s) */ 737 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 738 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 739 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 740 741 /* Create AP_loc for reuse */ 742 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 743 744 #if defined(PETSC_USE_INFO) 745 if (ao) { 746 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 747 } else { 748 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 749 } 750 ptap->AP_loc->info.mallocs = nspacedouble; 751 ptap->AP_loc->info.fill_ratio_given = fill; 752 ptap->AP_loc->info.fill_ratio_needed = apfill; 753 754 if (api[am]) { 755 ierr = PetscInfo3(ptap->AP_loc,"Nonscalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 756 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 757 } else { 758 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 759 } 760 #endif 761 762 /* (2-1) compute symbolic Co = Ro*AP_loc */ 763 /* ------------------------------------ */ 764 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 765 766 /* (3) send coj of C_oth to other processors */ 767 /* ------------------------------------------ */ 768 /* determine row ownership */ 769 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 770 rowmap->n = pn; 771 rowmap->bs = 1; 772 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 773 owners = rowmap->range; 774 775 /* determine the number of messages to send, their lengths */ 776 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 777 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 778 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 779 780 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 781 coi = c_oth->i; coj = c_oth->j; 782 con = ptap->C_oth->rmap->n; 783 proc = 0; 784 for (i=0; i<con; i++) { 785 while (prmap[i] >= owners[proc+1]) proc++; 786 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 787 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 788 } 789 790 len = 0; /* max length of buf_si[], see (4) */ 791 owners_co[0] = 0; 792 nsend = 0; 793 for (proc=0; proc<size; proc++) { 794 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 795 if (len_s[proc]) { 796 nsend++; 797 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 798 len += len_si[proc]; 799 } 800 } 801 802 /* determine the number and length of messages to receive for coi and coj */ 803 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 804 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 805 806 /* post the Irecv and Isend of coj */ 807 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 808 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 809 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 810 for (proc=0, k=0; proc<size; proc++) { 811 if (!len_s[proc]) continue; 812 i = owners_co[proc]; 813 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 814 k++; 815 } 816 817 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 818 /* ---------------------------------------- */ 819 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 820 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 821 822 /* receives coj are complete */ 823 for (i=0; i<nrecv; i++) { 824 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 825 } 826 ierr = PetscFree(rwaits);CHKERRQ(ierr); 827 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 828 829 /* add received column indices into ta to update Crmax */ 830 for (k=0; k<nrecv; k++) {/* k-th received message */ 831 Jptr = buf_rj[k]; 832 for (j=0; j<len_r[k]; j++) { 833 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 834 } 835 } 836 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 837 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 838 839 /* (4) send and recv coi */ 840 /*-----------------------*/ 841 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 842 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 843 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 844 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 845 for (proc=0,k=0; proc<size; proc++) { 846 if (!len_s[proc]) continue; 847 /* form outgoing message for i-structure: 848 buf_si[0]: nrows to be sent 849 [1:nrows]: row index (global) 850 [nrows+1:2*nrows+1]: i-structure index 851 */ 852 /*-------------------------------------------*/ 853 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 854 buf_si_i = buf_si + nrows+1; 855 buf_si[0] = nrows; 856 buf_si_i[0] = 0; 857 nrows = 0; 858 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 859 nzi = coi[i+1] - coi[i]; 860 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 861 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 862 nrows++; 863 } 864 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 865 k++; 866 buf_si += len_si[proc]; 867 } 868 for (i=0; i<nrecv; i++) { 869 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 870 } 871 ierr = PetscFree(rwaits);CHKERRQ(ierr); 872 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 873 874 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 875 ierr = PetscFree(len_ri);CHKERRQ(ierr); 876 ierr = PetscFree(swaits);CHKERRQ(ierr); 877 ierr = PetscFree(buf_s);CHKERRQ(ierr); 878 879 /* (5) compute the local portion of Cmpi */ 880 /* ------------------------------------------ */ 881 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 882 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 883 current_space = free_space; 884 885 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 886 for (k=0; k<nrecv; k++) { 887 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 888 nrows = *buf_ri_k[k]; 889 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 890 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 891 } 892 893 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 894 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 895 for (i=0; i<pn; i++) { 896 /* add C_loc into Cmpi */ 897 nzi = c_loc->i[i+1] - c_loc->i[i]; 898 Jptr = c_loc->j + c_loc->i[i]; 899 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 900 901 /* add received col data into lnk */ 902 for (k=0; k<nrecv; k++) { /* k-th received message */ 903 if (i == *nextrow[k]) { /* i-th row */ 904 nzi = *(nextci[k]+1) - *nextci[k]; 905 Jptr = buf_rj[k] + *nextci[k]; 906 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 907 nextrow[k]++; nextci[k]++; 908 } 909 } 910 nzi = lnk[0]; 911 912 /* copy data into free space, then initialize lnk */ 913 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 914 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 915 } 916 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 917 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 918 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 919 920 /* local sizes and preallocation */ 921 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 922 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 923 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 924 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 925 926 /* members in merge */ 927 ierr = PetscFree(id_r);CHKERRQ(ierr); 928 ierr = PetscFree(len_r);CHKERRQ(ierr); 929 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 930 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 931 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 932 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 933 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 934 935 /* attach the supporting struct to Cmpi for reuse */ 936 c = (Mat_MPIAIJ*)Cmpi->data; 937 c->ptap = ptap; 938 ptap->duplicate = Cmpi->ops->duplicate; 939 ptap->destroy = Cmpi->ops->destroy; 940 ptap->view = Cmpi->ops->view; 941 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 942 943 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 944 Cmpi->assembled = PETSC_FALSE; 945 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 946 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 947 *C = Cmpi; 948 PetscFunctionReturn(0); 949 } 950 951 952 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 953 { 954 PetscErrorCode ierr; 955 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 956 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 957 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 958 Mat_PtAPMPI *ptap = c->ptap; 959 Mat AP_loc,C_loc,C_oth; 960 PetscInt i,rstart,rend,cm,ncols,row; 961 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 962 PetscScalar *apa; 963 const PetscInt *cols; 964 const PetscScalar *vals; 965 966 PetscFunctionBegin; 967 ierr = MatZeroEntries(C);CHKERRQ(ierr); 968 /* 1) get R = Pd^T,Ro = Po^T */ 969 if (ptap->reuse == MAT_REUSE_MATRIX) { 970 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 971 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 972 } 973 974 /* 2) get AP_loc */ 975 AP_loc = ptap->AP_loc; 976 ap = (Mat_SeqAIJ*)AP_loc->data; 977 978 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 979 /*-----------------------------------------------------*/ 980 if (ptap->reuse == MAT_REUSE_MATRIX) { 981 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 982 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 983 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 984 } 985 986 /* 2-2) compute numeric A_loc*P - dominating part */ 987 /* ---------------------------------------------- */ 988 /* get data from symbolic products */ 989 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 990 if (ptap->P_oth) { 991 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 992 } 993 apa = ptap->apa; 994 api = ap->i; 995 apj = ap->j; 996 for (i=0; i<am; i++) { 997 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 998 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 999 apnz = api[i+1] - api[i]; 1000 for (j=0; j<apnz; j++) { 1001 col = apj[j+api[i]]; 1002 ap->a[j+ap->i[i]] = apa[col]; 1003 apa[col] = 0.0; 1004 } 1005 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 1006 } 1007 1008 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 1009 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 1010 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 1011 C_loc = ptap->C_loc; 1012 C_oth = ptap->C_oth; 1013 1014 /* add C_loc and Co to to C */ 1015 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1016 1017 /* C_loc -> C */ 1018 cm = C_loc->rmap->N; 1019 c_seq = (Mat_SeqAIJ*)C_loc->data; 1020 cols = c_seq->j; 1021 vals = c_seq->a; 1022 1023 1024 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 1025 /* when there are no off-processor parts. */ 1026 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 1027 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 1028 /* a table, and other, more complex stuff has to be done. */ 1029 if (C->assembled) { 1030 C->was_assembled = PETSC_TRUE; 1031 C->assembled = PETSC_FALSE; 1032 } 1033 if (C->was_assembled) { 1034 for (i=0; i<cm; i++) { 1035 ncols = c_seq->i[i+1] - c_seq->i[i]; 1036 row = rstart + i; 1037 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1038 cols += ncols; vals += ncols; 1039 } 1040 } else { 1041 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 1042 } 1043 1044 /* Co -> C, off-processor part */ 1045 cm = C_oth->rmap->N; 1046 c_seq = (Mat_SeqAIJ*)C_oth->data; 1047 cols = c_seq->j; 1048 vals = c_seq->a; 1049 for (i=0; i<cm; i++) { 1050 ncols = c_seq->i[i+1] - c_seq->i[i]; 1051 row = p->garray[i]; 1052 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1053 cols += ncols; vals += ncols; 1054 } 1055 1056 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1057 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1058 1059 ptap->reuse = MAT_REUSE_MATRIX; 1060 PetscFunctionReturn(0); 1061 } 1062